I'll just add that it is always a really good idea to view the trees you
(think you) are using, not just rely on the variance-covariance matrices
derived from them and used in PGLS analyses, etc. Several times when I
was compiling trees and data from the literature authors sent me tree
files (e.g., Nexus) that did not match what they showed in a paper or
described in the methods. Sometimes this was because the
default display in Mesquite is NOT "branches proportional to lengths,"
but I am sure potentially misleading displays occur in some other
programs as well.

If one does force a tree to become ultrametric, then make sure you
provide that tree and the original in the Online Supplemental Material
or whatever, and clearly say what you did.

I haven't been closing following this thread, so I'm not sure that
this is relevant - but phytools has a function called
'force.ultrametric' (I believe) that does precisely what its name
suggests it might.
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/
<http://faculty.umb.edu/liam.revell/>
On 5/3/2018 3:34 PM, David Bapst wrote:
Hmm. I hope that isn't the case - branching.times() is used pretty
widely in ape-dependent packages for getting node ages from dated
ultrametric trees, and if such minimally non-ultrametric trees can
cause branching.times throw negative node ages, then I'm really
concerned what impact that might have elsewhere in the R-phylo
universe.
-Dave
On Wed, May 2, 2018 at 2:30 PM, Brian O'Meara <bome...@utk.edu
<mailto:bome...@utk.edu>> wrote:
On Wed, May 2, 2018 at 2:53 PM, David Bapst
<dwba...@tamu.edu <mailto:dwba...@tamu.edu>> wrote:
Given that your tree appears to be non-ultrametric
enough to cause
branching.times to throw some nonsensical node ages, if
it is supposed
to be ultrametric. I recommend checking it carefully to
figure out why
the tips seem to not quite be at the same distance from
the root.
Sometimes this happens with tree import from a file -- it
could be a newick
tree with branch lengths precise to the hundredths but a lot
of the R
ultrametric tests by default use higher precision (1e-08, iirc).
Best,
Brian
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